Molecular recognition by proteins is fundamental to almost every biological process, particularly the protein associations underlying cellular signal transduction. Understanding the basis for protein-protein interactions requires the full characterization of the thermodynamics of their association. Historically it has been virtually impossible to experimentally estimate changes in protein conformational entropy, a potentially important component of the free energy of protein association.
Numerous structural studies have revealed that protein-protein interfaces often involve dozens of amino acid residues and thousands of Å2 of contact area. Wodak, S. J. & Janin, J. Structural basis of macromolecular recognition. Adv. Prot. Chem. 61, 9-73 (2002). It has also become apparent that a non-uniform contribution of individual residues to the free energy of binding can exist and that static structural analyses can mask important factors underlying the high-affinity interactions between proteins. Clackson, T. & Wells, J. A. A hot spot of binding energy in a hormone-receptor interface. Science 267, 383-386 (1995). Of particular interest is the role of protein conformational entropy in modulating the free energy of the association of a protein with a ligand. A simplistic decomposition emphasizes the fact that the entropy of binding (ΔSbind), obtainable by calorimetric methods, is comprised of contributions associated with the protein, the ligand and the solvent:ΔGbind=ΔHbind−TΔSbind=ΔHbindT(ΔSprotein+ΔSligand+ΔSsolvent)  (1)
It is well established that the transitions of a ligand from a disordered (high entropy) unbound state to a structured (lower entropy) bound state can profoundly influence the entropy of macromolecular associations. Spolar, R. S. & Record, M. T. Coupling of local folding to site-specific binding of proteins to DNA. Science 263, 777-784. It is also well established that burial of hydrophobic surface area and the consequent release of hydration waters to the bulk solvent can also contribute significantly to the thermodynamics of binding. Sturtevant, J. M. Heat capacity and entropy changes in processes involving proteins. Proc. Natl Acad. Sci. USA 74, 2236-2240 (1977). What is less understood is the potential entropic contributions from a ‘structured’ protein (ΔSprotein), 5 which includes changes in its conformational entropy (ΔSconf) as well as changes in rotational and translational entropy. Steinberg, I. Z. & Scheraga, H. A. Entropy changes accompanying association reactions of proteins. J. Biol. Chem. 238, 172-181 (1963); Cooper, A. & Dryden, D. T. F. Allostery without conformational change—a plausible model. Eur. Biophys. J. Biophys. Lett. 11, 103-109 (1984); Karplus, M., Ichiye, T & Pettitt, B. M. Configurational entropy of native proteins. Biophys. J. 52, 1083-1085 (1987).